Optimization of gene expression microarray protocol for formalin-fixed paraffin-embedded tissues.
Optimization of gene expression microarray protocol for formalin-fixed paraffin-embedded tissues.
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DOI：
10.1016/j.gdata.2016.02.006
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发表时间：
2016-03
期刊：
影响因子：
--
通讯作者：
Özdağ H
中科院分区：
文献类型：
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作者：
Belder N;Coşkun Ö;Erdoğan BD;Savaş B;Ensari A;Özdağ H
福尔马林固定石蜡包埋（FFPE）组织是一种广泛用于回顾性研究的临床标本。FFPE样本长期临床随访的可能性使其成为评估分子和临床信息之间联系的有价值来源。在分子研究领域，特别是使用高通量分子技术，如微阵列基因表达谱，FFPE样品的工作已经变得突出。由于福尔马林固定过程的有害影响，如核酸的降解，与蛋白质的交联，以及对DNA和RNA的化学修饰，使用FFPE样品进行基因表达谱研究存在一些限制。迄今为止，已经进行了许多研究以使用微阵列评估基因表达谱（托马斯等人，托马斯等人（2013）; Scicchitano等人，Scicchitano等人（2006）; Frank等人，Frank等人（2007年）; Fedorowicz等人，Fedorowicz等人（2009））。然而，对于FFPE样品的微阵列分析仍然没有普遍接受的、有效的和标准化的程序。本文介绍了在我们最近接受发表的文章中提出的微阵列数据，该文章显示了从FFPE组织切片脱蜡和RNA提取到微阵列基因表达分析的标准协议。在这里，我们详细介绍了我们的数据，存放在基因表达综合（GEO）数据库中，登录号为GSE 73883。评价了两种不同cRNA/cDNA制备和标记方案与两种不同阵列平台（Affyphase Human Genome U133 Plus 2.0和U133_X3P）的四种组合，以确定哪种组合给出了最佳的当前调用百分比。该研究提供了一个用于比较分析的数据集，该数据集有可能为FFPE组织样本的基因表达谱分析提供一个强大的方案。
Formalin-fixed paraffin-embedded (FFPE) tissue is a widely available clinical specimen for retrospective studies. The possibility of long-term clinical follow-up of FFPE samples makes them a valuable source to evaluate links between molecular and clinical information. Working with FFPE samples in the molecular research area, especially using high-throughput molecular techniques such as microarray gene expression profiling, has come into prominence. Because of the harmful effects of formalin fixation process such as degradation of nucleic acids, cross-linking with proteins, and chemical modifications on DNA and RNA, there are some limitations in gene expression profiling studies using FFPE samples. To date many studies have been conducted to evaluate gene expression profiling using microarrays (Thomas et al., Thomas et al. (2013); Scicchitano et al., Scicchitano et al. (2006); Frank et al., Frank et al. (2007); Fedorowicz et al., Fedorowicz et al. (2009)). However, there is still no generally accepted, efficient and standardized procedure for microarray analysis of FFPE samples. This paper describes the microarray data presented in our recently accepted to be published article showing a standard protocol from deparaffinization of FFPE tissue sections and RNA extraction to microarray gene expression analysis. Here we represent our data in detail, deposited in the gene expression omnibus (GEO) database with the accession number GSE73883. Four combinations of two different cRNA/cDNA preparation and labeling protocols with two different array platforms (Affymetrix Human Genome U133 Plus 2.0 and U133_X3P) were evaluated to determine which combination gives the best percentage of present call. The study presents a dataset for comparative analysis which has a potential in terms of providing a robust protocol for gene expression profiling with FFPE tissue samples.